
library(tidyverse)
library(Seurat)
library(RColorBrewer)
library(future)
#for 200gb ram 
options(future.globals.maxSize = 200000 * 1024^2)

── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──

✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.6     ✔ dplyr   1.0.7
✔ tidyr   1.1.4     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.1

── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()


library(ggplot2)


## Load BR_time_course downloaded from GEO:GSE212230
rc.integrated <- readRDS("../../../kallisto-bus/output/Integration/BR_time_course.rds")


# BRZ
brz <- subset(rc.integrated, cells=c('CAACAACTCGCCGAAC_6','AAAGGTATCTCACTCG_1',colnames(rc.integrated)[which((rc.integrated$orig.ident=="sc_43")|(rc.integrated$orig.ident=="sc_50"))]))


table(brz$orig.ident)

sc_12 sc_43 sc_44 sc_50 
    1  8874     1  5087


Idents(brz) <- "time.celltype.anno.Li.crude"
DefaultAssay(brz) <- "integrated"


brz@assays$integrated@scale.data[,'CAACAACTCGCCGAAC_6'] <- rep(0,17732)
brz@assays$integrated@data[,'CAACAACTCGCCGAAC_6'] <- rep(0,17732)
brz@assays$integrated@scale.data[,'AAAGGTATCTCACTCG_1'] <- rep(0,17732)
brz@assays$integrated@data[,'AAAGGTATCTCACTCG_1'] <- rep(0,17732)


# BL 2 hours
bl2 <- subset(rc.integrated, cells=c('CAACAACTCGCCGAAC_6',colnames(rc.integrated)[which((rc.integrated$orig.ident=="sc_46")|(rc.integrated$orig.ident=="sc_49"))]))


table(bl2$orig.ident)

sc_44 sc_46 sc_49 
    1  6847  5638


Idents(bl2) <- "time.celltype.anno.Li.crude"
DefaultAssay(bl2) <- "integrated"

bl2

An object of class Seurat 
71231 features across 12486 samples within 3 assays 
Active assay: integrated (17732 features, 17732 variable features)
 2 other assays present: RNA, SCT
 4 dimensional reductions calculated: pca, umap, umap_3D, umap_2D


bl2@assays$integrated@scale.data[,'CAACAACTCGCCGAAC_6'] <- rep(0,17732)
bl2@assays$integrated@data[,'CAACAACTCGCCGAAC_6'] <- rep(0,17732)


## Load libraries
library(cowplot)
library(ComplexHeatmap)
library(circlize)
library(GeneOverlap)
library(gprofiler2)
library(ggrepel)
library(ggplot2)

Loading required package: grid

========================================
ComplexHeatmap version 2.6.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================


========================================
circlize version 0.4.12
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================


## Load root atlas downloed from GEO:GSE152766
rc.integrated <- readRDS("../../../kallisto-bus/output/Integration/./Root_Atlas_seu4.rds")


## Downloaded from https://github.com/ohlerlab/COPILOT/tree/master/supp_data
(used.markers <- read_csv("../Validated_Markers.csv"))

── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
cols(
  Locus = col_character(),
  Gene = col_character(),
  Celltype = col_character(),
  Source = col_character()
)


used.markers <- used.markers[-c(3,5,6,7,9,11,12,20,26,27,28,38,39),]


used.markers


used.markers <- rbind(used.markers, c("AT2G36100", "CASP1", "Endodermis", "Trevor"))
used.markers <- rbind(used.markers, c("AT5G64620", "C/VIF2", "Cortex", "Trevor"))


## DE results table from Shahan & Hsu 2022
(Markers_to_plot <- read_csv("../Atlas_time_celltype_Clust_Markers_crude.csv"))

── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
cols(
  p_val = col_double(),
  avg_logFC = col_double(),
  pct.1 = col_double(),
  pct.2 = col_double(),
  p_val_adj = col_double(),
  cluster = col_character(),
  gene = col_character(),
  Name = col_character()
)


Markers_to_plot <- Markers_to_plot %>% mutate(pct.diff = pct.1-pct.2) %>% mutate(pct.diff.rank = rank(pct.diff)) %>% mutate(avg_logFC.rank = rank(avg_logFC)) %>% mutate(combined.rank = pct.diff.rank+avg_logFC.rank) %>% filter(p_val_adj<=0.01)


Markers_to_plot[which(Markers_to_plot$Name=="SCR"),]


vMarkers_to_plot <- Markers_to_plot[(Markers_to_plot$gene %in% used.markers$Locus),]


Markers_to_plot[which(Markers_to_plot$Name=="CASP1"),]


Markers_to_plot[which(Markers_to_plot$Name=="C/VIF2"),]


vMarkers_to_plot


vMarkers_to_plot <- vMarkers_to_plot %>% group_by(gene) %>% top_n(1, combined.rank)  %>% group_by(cluster) %>% top_n(1, combined.rank) %>% mutate(source=1)


iMarkers_to_plot <- Markers_to_plot %>% group_by(gene) %>% top_n(1, combined.rank)  %>% group_by(cluster) %>% top_n(1, combined.rank) %>% mutate(source=2)


Markers_to_plot <- bind_rows(vMarkers_to_plot,iMarkers_to_plot)


Markers_to_plot <- Markers_to_plot %>% group_by(cluster) %>% top_n(1,-source)


Markers_to_plot <- Markers_to_plot %>% mutate(timezone=gsub("_.*$","",cluster)) %>% mutate(celltype=gsub("^.*_","",cluster))


Markers_to_plot


order <- c("Proliferation Domain_Quiescent Center","Proximal Columella","Distal Columella", "Proximal Lateral Root Cap", "Distal Lateral Root Cap", 
           "Proliferation Domain_Atrichoblast","Transition Domain_Atrichoblast","Elongation_Atrichoblast","Maturation_Atrichoblast",
          "Proliferation Domain_Trichoblast", "Transition Domain_Trichoblast", "Elongation_Trichoblast", "Maturation_Trichoblast",
          "Proliferation Domain_Cortex", "Transition Domain_Cortex", "Elongation_Cortex", "Maturation_Cortex",
          "Proliferation Domain_Endodermis","Transition Domain_Endodermis", "Elongation_Endodermis", "Maturation_Endodermis",
          "Proliferation Domain_Procambium", "Transition Domain_Procambium", "Elongation_Procambium", "Maturation_Procambium", 
          "Proliferation Domain_Pericycle", "Transition Domain_Pericycle", "Elongation_Pericycle", "Maturation_Pericycle",
          "Proliferation Domain_Phloem", "Transition Domain_Phloem", "Elongation_Phloem", "Maturation_Phloem",
          "Proliferation Domain_Xylem", "Transition Domain_Xylem", "Elongation_Xylem", "Maturation_Xylem")


Markers_to_plot <- Markers_to_plot[match(order, Markers_to_plot$cluster),]


(c_levels <- unique(Markers_to_plot$cluster))


ct_to_plt_Names <- rev(Markers_to_plot$Name)
ct_to_plt_genes <- rev(Markers_to_plot$gene)


(labels <- (ct_to_plt_Names))


table(rc.integrated$time.celltype.anno.Li.crude)

Proliferation Domain_Quiescent Center                    Proximal Columella 
                                   91                                  1282 
                     Distal Columella             Proximal Lateral Root Cap 
                                 5846                                 16790 
              Distal Lateral Root Cap     Proliferation Domain_Atrichoblast 
                                 4864                                  3725 
       Transition Domain_Atrichoblast               Elongation_Atrichoblast 
                                 2354                                  3772 
              Maturation_Atrichoblast      Proliferation Domain_Trichoblast 
                                 2434                                  1648 
        Transition Domain_Trichoblast                Elongation_Trichoblast 
                                 2514                                  3492 
               Maturation_Trichoblast           Proliferation Domain_Cortex 
                                 3560                                   696 
             Transition Domain_Cortex                     Elongation_Cortex 
                                 2121                                  4123 
                    Maturation_Cortex       Proliferation Domain_Endodermis 
                                 1124                                   921 
         Transition Domain_Endodermis                 Elongation_Endodermis 
                                   40                                  5042 
                Maturation_Endodermis       Proliferation Domain_Procambium 
                                 2327                                     5 
         Transition Domain_Procambium                 Elongation_Procambium 
                                   55                                  7793 
                Maturation_Procambium        Proliferation Domain_Pericycle 
                                 1420                                   237 
          Transition Domain_Pericycle                  Elongation_Pericycle 
                                  338                                  9681 
                 Maturation_Pericycle           Proliferation Domain_Phloem 
                                 1746                                    49 
             Transition Domain_Phloem                     Elongation_Phloem 
                                  378                                  2393 
                    Maturation_Phloem            Proliferation Domain_Xylem 
                                  296                                   107 
              Transition Domain_Xylem                      Elongation_Xylem 
                                   66                                  3052 
                     Maturation_Xylem 
                                  554


order


## BL2
bl2$time.celltype.anno.Li.crude <- factor(bl2$time.celltype.anno.Li.crude, levels = order[sort(match(unique(bl2$time.celltype.anno.Li.crude),order))])

options(repr.plot.width=14, repr.plot.height=10)

DotPlot(object = bl2, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + 
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")+scale_y_discrete(breaks=order, labels=order) + ylab("")


options(repr.plot.width=14, repr.plot.height=10)
dot <- DotPlot(object = bl2, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + ylab("")  + theme(axis.title.y=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank()) + 
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")
dot


options(repr.plot.width=14, repr.plot.height=10)
dot <- dot + geom_rect(xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = 1.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 1.5, xmax = 3.5, ymin = 1.5, ymax = 3.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 3.5, xmax = 5.5, ymin = 3.5, ymax = 5.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 5.5, xmax = 9.5, ymin = 5.5, ymax = 9.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 9.5, xmax = 13.5, ymin = 9.5, ymax = 13.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 13.5, xmax = 17.5, ymin = 13.5, ymax = 17.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 17.5, xmax = 21.5, ymin = 17.5, ymax = 21.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 21.5, xmax = 25.5, ymin = 21.5, ymax = 25.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 25.5, xmax = 29.5, ymin = 25.5, ymax = 29.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 29.5, xmax = 33.5, ymin = 29.5, ymax = 33.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 33.5, xmax = 37.5, ymin = 33.5, ymax = 37.5, alpha = 0,fill=alpha("grey",0), color="black") 
#geom_rect(xmin = 37.5, xmax = 41.5, ymin = 37.5, ymax = 41.5, alpha = 0,fill=alpha("grey",0), color="black") + 
#geom_rect(xmin = 41.5, xmax = 45.5, ymin = 41.5, ymax = 45.5, alpha = 0,fill=alpha("grey",0), color="black") + 
#geom_rect(xmin = 45.5, xmax = 49.5, ymin = 45.5, ymax = 49.5, alpha = 0,fill=alpha("grey",0), color="black")

dot


ggsave("../BL_2hours_cell_dev_marker_dot_20220808.pdf", width=12, height=10)


## BRZ
brz$time.celltype.anno.Li.crude <- factor(brz$time.celltype.anno.Li.crude, levels = order[sort(match(unique(brz$time.celltype.anno.Li.crude),order))])


options(repr.plot.width=14, repr.plot.height=10)

DotPlot(object = brz, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + 
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")


options(repr.plot.width=14, repr.plot.height=10)
dot <- DotPlot(object = brz, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + ylab("")  + theme(axis.title.y=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank()) + 
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")
dot


options(repr.plot.width=14, repr.plot.height=10)
dot <- dot + geom_rect(xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = 1.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 1.5, xmax = 3.5, ymin = 1.5, ymax = 3.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 3.5, xmax = 5.5, ymin = 3.5, ymax = 5.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 5.5, xmax = 9.5, ymin = 5.5, ymax = 9.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 9.5, xmax = 13.5, ymin = 9.5, ymax = 13.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 13.5, xmax = 17.5, ymin = 13.5, ymax = 17.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 17.5, xmax = 21.5, ymin = 17.5, ymax = 21.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 21.5, xmax = 25.5, ymin = 21.5, ymax = 25.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 25.5, xmax = 29.5, ymin = 25.5, ymax = 29.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 29.5, xmax = 33.5, ymin = 29.5, ymax = 33.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 33.5, xmax = 37.5, ymin = 33.5, ymax = 37.5, alpha = 0,fill=alpha("grey",0), color="black") 
#geom_rect(xmin = 37.5, xmax = 41.5, ymin = 37.5, ymax = 41.5, alpha = 0,fill=alpha("grey",0), color="black") + 
#geom_rect(xmin = 41.5, xmax = 45.5, ymin = 41.5, ymax = 45.5, alpha = 0,fill=alpha("grey",0), color="black") + 
#geom_rect(xmin = 45.5, xmax = 49.5, ymin = 45.5, ymax = 49.5, alpha = 0,fill=alpha("grey",0), color="black")

dot


ggsave("../BRZ_cell_dev_marker_dot_20220808.pdf", width=12, height=10)


## BL time course
Idents(rc.integrated) <- "time.celltype.anno.Li.crude"
DefaultAssay(rc.integrated) <- "integrated"
rc.integrated$time.celltype.anno.Li.crude <- factor(rc.integrated$time.celltype.anno.Li.crude, levels = order[sort(match(unique(rc.integrated$time.celltype.anno.Li.crude),order))])


options(repr.plot.width=14, repr.plot.height=10)

DotPlot(object = rc.integrated, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + 
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")


options(repr.plot.width=14, repr.plot.height=10)
dot <- DotPlot(object = rc.integrated, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + ylab("")  + theme(axis.title.y=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank()) + 
scale_x_discrete(breaks=ct_to_plt_genes, labels=labels) + xlab("")
dot


options(repr.plot.width=14, repr.plot.height=10)
dot <- dot + geom_rect(xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = 1.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 1.5, xmax = 3.5, ymin = 1.5, ymax = 3.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 3.5, xmax = 5.5, ymin = 3.5, ymax = 5.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 5.5, xmax = 9.5, ymin = 5.5, ymax = 9.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 9.5, xmax = 13.5, ymin = 9.5, ymax = 13.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 13.5, xmax = 17.5, ymin = 13.5, ymax = 17.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 17.5, xmax = 21.5, ymin = 17.5, ymax = 21.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 21.5, xmax = 25.5, ymin = 21.5, ymax = 25.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 25.5, xmax = 29.5, ymin = 25.5, ymax = 29.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 29.5, xmax = 33.5, ymin = 29.5, ymax = 33.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 33.5, xmax = 37.5, ymin = 33.5, ymax = 37.5, alpha = 0,fill=alpha("grey",0), color="black") 
#geom_rect(xmin = 37.5, xmax = 41.5, ymin = 37.5, ymax = 41.5, alpha = 0,fill=alpha("grey",0), color="black") + 
#geom_rect(xmin = 41.5, xmax = 45.5, ymin = 41.5, ymax = 45.5, alpha = 0,fill=alpha("grey",0), color="black") + 
#geom_rect(xmin = 45.5, xmax = 49.5, ymin = 45.5, ymax = 49.5, alpha = 0,fill=alpha("grey",0), color="black")

dot


## WT atlas
Idents(rc.integrated) <- "time.celltype.anno.Li.crude"
DefaultAssay(rc.integrated) <- "integrated"


rc.integrated$time.celltype.anno.Li.crude <- factor(rc.integrated$time.celltype.anno.Li.crude, levels = order[sort(match(unique(rc.integrated$time.celltype.anno.Li.crude),order))])


options(repr.plot.width=14, repr.plot.height=10)

DotPlot(object = rc.integrated, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + 
scale_x_discrete(breaks=breaks, labels=labels) + xlab("")


options(repr.plot.width=14, repr.plot.height=10)
dot <- DotPlot(object = rc.integrated, features = ct_to_plt_genes, cols = c("white", "red")) + RotatedAxis() + ylab("")  + theme(axis.title.y=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank()) + 
scale_x_discrete(breaks=breaks, labels=labels) + xlab("")
dot


options(repr.plot.width=14, repr.plot.height=10)
dot <- dot + geom_rect(xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = 1.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 1.5, xmax = 3.5, ymin = 1.5, ymax = 3.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 3.5, xmax = 5.5, ymin = 3.5, ymax = 5.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 5.5, xmax = 9.5, ymin = 5.5, ymax = 9.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 9.5, xmax = 13.5, ymin = 9.5, ymax = 13.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 13.5, xmax = 17.5, ymin = 13.5, ymax = 17.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 17.5, xmax = 21.5, ymin = 17.5, ymax = 21.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 21.5, xmax = 25.5, ymin = 21.5, ymax = 25.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 25.5, xmax = 29.5, ymin = 25.5, ymax = 29.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 29.5, xmax = 33.5, ymin = 29.5, ymax = 33.5, alpha = 0,fill=alpha("grey",0), color="black") + 
geom_rect(xmin = 33.5, xmax = 37.5, ymin = 33.5, ymax = 37.5, alpha = 0,fill=alpha("grey",0), color="black") 
#geom_rect(xmin = 37.5, xmax = 41.5, ymin = 37.5, ymax = 41.5, alpha = 0,fill=alpha("grey",0), color="black") + 
#geom_rect(xmin = 41.5, xmax = 45.5, ymin = 41.5, ymax = 45.5, alpha = 0,fill=alpha("grey",0), color="black") + 
#geom_rect(xmin = 45.5, xmax = 49.5, ymin = 45.5, ymax = 49.5, alpha = 0,fill=alpha("grey",0), color="black")

dot


ann_df <- tibble(timezone=as.character(Markers_to_plot$timezone), 
                celltype= as.character(Markers_to_plot$celltype)) %>% 
mutate(row=dplyr::row_number(), 
col=rep("A")) %>%
group_by(celltype) %>%
mutate(ct_row=dplyr::row_number()) %>%
ungroup() %>%
mutate(Label=celltype)

#ann_df$Label[ann_df$celltype=="Metaphloem & Companion Cell"] <- "Metaphloem & CC"
ann_df$Label[ann_df$ct_row!=3] <- " "
ann_df$Label[ann_df$celltype=="Quiescent Center"] <- "Quiescent Center"
ann_df$Label[(ann_df$celltype=="Columella") & (ann_df$ct_row==2)] <- "Columella"
ann_df$Label[(ann_df$celltype=="Lateral Root Cap") & (ann_df$ct_row==2)] <- "Lateral Root Cap"


ann_df$row <- factor(ann_df$row)
ann_df$timezone <- factor(ann_df$timezone, levels=c("Proliferation Domain", "Transition Domain", "Elongation", "Maturation", "Proximal Lateral Root Cap", "Distal Lateral Root Cap", "Proximal Columella", "Distal Columella"))


options(repr.plot.width=1, repr.plot.height=10)
(time_ann_p <- ann_df %>% ggplot(aes(x=col, y=row, fill=timezone)) + geom_tile() + scale_fill_manual(values = c('#F7E7B0','#FFC400','#2B871F','#005E3B',"#deebf7", "#3182bd", '#fee0d2','#de2d26')) +theme_nothing())


options(repr.plot.width=3, repr.plot.height=10)
ann_df %>% ggplot(aes(x=col, y=row, fill=timezone)) + geom_tile() + scale_fill_manual(values = c('#F7E7B0','#FFC400','#2B871F','#005E3B',"#deebf7", "#3182bd", '#fee0d2','#de2d26')) + theme_minimal()


order <- c("Quiescent Center", "Ground Tissue","Columella", "Lateral Root Cap", "Atrichoblast", "Trichoblast", "Cortex", "Endodermis", "Phloem","Protophloem", "Xylem", "Procambium","Pericycle","Phloem Pole Pericycle", "Protoxylem", "Metaxylem", "Unknown")
palette <- c("#9400d3", "#DCD0FF","#5ab953", "#bfef45", "#008080", "#21B6A8", "#82b6ff", "#0000FF","#e6194b", "#dd77ec", "#9a6324", "#ffe119", "#ff9900", "#ffd4e3", "#9a6324", "#ddaa6f", "#EEEEEE")


options(repr.plot.width=1, repr.plot.height=10)

ann_df$celltype <- factor(ann_df$celltype, levels = order[sort(match(unique(ann_df$celltype),order))])

color <- palette[sort(match(unique(ann_df$celltype),order))]

(cell_ann_p <- ann_df %>% ggplot(aes(x=col, y=row, fill=celltype)) + geom_tile() + scale_fill_manual(values = color) + theme_nothing())


options(repr.plot.width=1, repr.plot.height=10)
cell_ann_p | time_ann_p


options(repr.plot.width=3.5, repr.plot.height=10)
(text_ann_p <- ann_df %>% ggplot(aes(x=col, y=row, label=Label)) + geom_text(size = 4) + theme(plot.margin = margin(0, 0, 35, 35, "cm")) + theme_nothing())


options(repr.plot.width=4, repr.plot.height=10)
(c_ann <- text_ann_p | (cell_ann_p | time_ann_p))


# BL 2 hours
options(repr.plot.width=15, repr.plot.height=10)
combined_marker_plot <- text_ann_p + cell_ann_p + time_ann_p + dot + patchwork
combined_marker_plot


ggsave("../BL_2hours_cell_dev_marker_dot_20220808.pdf", width=15, height=10)


# BRZ
options(repr.plot.width=15, repr.plot.height=10)
combined_marker_plot <- text_ann_p + cell_ann_p + time_ann_p + dot + patchwork::plot_layout(widths = c(0.8,0.2,0.2,4), nrow=1)
combined_marker_plot


ggsave("../BRZ_cell_dev_marker_dot_20220808.pdf", width=15, height=10)


## BL time course
options(repr.plot.width=15, repr.plot.height=10)
combined_marker_plot <- text_ann_p + cell_ann_p + time_ann_p + dot + patchwork::plot_layout(widths = c(0.8,0.2,0.2,4), nrow=1)
combined_marker_plot


## WT atlas
options(repr.plot.width=15, repr.plot.height=10)
combined_marker_plot <- text_ann_p + cell_ann_p + time_ann_p + dot + patchwork::plot_layout(widths = c(0.8,0.2,0.2,4), nrow=1)
combined_marker_plot


ggsave("../Atlas_cell_dev_marker_dot_20220310.pdf", width=15, height=10)


sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS/LAPACK: /home/tmnolan7/anaconda3/envs/r_3.6.1/lib/libopenblasp-r0.3.7.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] ggrepel_0.8.2        gprofiler2_0.1.8     GeneOverlap_1.22.0  
 [4] circlize_0.4.8       ComplexHeatmap_2.2.0 cowplot_1.0.0       
 [7] future_1.17.0        RColorBrewer_1.1-2   Seurat_3.1.5        
[10] forcats_0.5.0        stringr_1.4.0        dplyr_0.8.5         
[13] purrr_0.3.3          readr_1.3.1          tidyr_1.0.2         
[16] tibble_3.0.1         ggplot2_3.3.0        tidyverse_1.3.0     

loaded via a namespace (and not attached):
  [1] Rtsne_0.15           colorspace_1.4-1     rjson_0.2.20        
  [4] ellipsis_0.3.0       ggridges_0.5.2       IRdisplay_0.7.0     
  [7] GlobalOptions_0.1.1  base64enc_0.1-3      fs_1.4.1            
 [10] clue_0.3-57          rstudioapi_0.11      farver_2.0.3        
 [13] leiden_0.3.3         listenv_0.8.0        npsurv_0.4-0        
 [16] fansi_0.4.1          lubridate_1.7.8      xml2_1.3.0          
 [19] codetools_0.2-16     splines_3.6.1        lsei_1.2-0          
 [22] IRkernel_1.1         jsonlite_1.6.1       broom_0.5.5         
 [25] ica_1.0-2            cluster_2.1.0        dbplyr_1.4.2        
 [28] png_0.1-7            uwot_0.1.8           sctransform_0.2.1   
 [31] compiler_3.6.1       httr_1.4.1           backports_1.1.7     
 [34] assertthat_0.2.1     Matrix_1.2-18        lazyeval_0.2.2      
 [37] cli_2.0.2            htmltools_0.4.0      tools_3.6.1         
 [40] rsvd_1.0.3           igraph_1.2.5         gtable_0.3.0        
 [43] glue_1.4.1           RANN_2.6.1           reshape2_1.4.3      
 [46] rappdirs_0.3.1       Rcpp_1.0.4.6         cellranger_1.1.0    
 [49] vctrs_0.2.4          gdata_2.18.0         ape_5.3             
 [52] nlme_3.1-145         lmtest_0.9-37        globals_0.12.5      
 [55] rvest_0.3.5          lifecycle_0.2.0      irlba_2.3.3         
 [58] gtools_3.8.2         MASS_7.3-51.5        zoo_1.8-8           
 [61] scales_1.1.1         hms_0.5.3            parallel_3.6.1      
 [64] gridExtra_2.3        reticulate_1.15      pbapply_1.4-2       
 [67] stringi_1.4.3        caTools_1.18.0       shape_1.4.4         
 [70] repr_1.1.0           rlang_0.4.6          pkgconfig_2.0.3     
 [73] bitops_1.0-6         evaluate_0.14        lattice_0.20-41     
 [76] ROCR_1.0-7           labeling_0.3         patchwork_1.0.0.9000
 [79] htmlwidgets_1.5.1    tidyselect_1.0.0     RcppAnnoy_0.0.16    
 [82] plyr_1.8.6           magrittr_1.5         R6_2.4.1            
 [85] gplots_3.0.3         generics_0.0.2       pbdZMQ_0.3-3        
 [88] DBI_1.1.0            pillar_1.4.3         haven_2.2.0         
 [91] withr_2.2.0          fitdistrplus_1.0-14  RCurl_1.98-1.2      
 [94] survival_3.1-11      tsne_0.1-3           future.apply_1.4.0  
 [97] modelr_0.1.6         crayon_1.3.4         uuid_0.1-4          
[100] KernSmooth_2.23-16   plotly_4.9.2.1       GetoptLong_0.1.8    
[103] readxl_1.3.1         data.table_1.12.8    reprex_0.3.0        
[106] digest_0.6.25        munsell_0.5.0        viridisLite_0.3.0

Locus	Gene	Celltype	Source
<chr>	<chr>	<chr>	<chr>
AT1G79840	GL2	Atrichoblast	Lee et al., PNAS, 2006
AT3G28540	AT3G28540	Columella (1-3th Outer Layer)	Wendrich et al., Science, 2020
AT5G48130	AT5G48130	Columella (1-4th Outer Layer) + LRC (3 Vertical Layers from Columella)	Wendrich et al., Science, 2020
AT1G17400	AT1G17400	Columella (1-5th Outer Layer)	Wendrich et al., Science, 2020
AT1G33280	BRN1	Columella (1st Outer Layer) + LRC (1st +2nd Outer Layer)	Kamiya et al., Development, 2016
AT4G10350	BRN2	Columella (1st Outer Layer) + LRC (1st Outer Layer)	Kamiya et al., Development, 2016
AT1G79580	SMB	Columella + LRC	Kamiya et al., Development, 2016
AT1G62500	CO2	Cortex	Heidstra et al., GenesDev, 2004
AT1G62510	AT1G62510	Cortex	Denyer et al., Dev Cell, 2019
AT2G40260	AT2G40260	Cortex	Wendrich et al., Science, 2020
AT2G29330	TRI	Cortex + Endodermis	Wendrich et al., Science, 2020
AT3G56220	AT3G56220	Cortex + Endodermis	Wendrich et al., Science, 2020
AT3G61930	AT3G61930	Distal Columella	SEMITONES
AT1G16390	AT1G16390	Endodermis	Wendrich et al., Science, 2020
AT1G30750	AT1G30750	Endodermis	Wendrich et al., Science, 2020
AT3G54220	SCR	Endodermis	Birnbaum et al., Science, 2003
AT4G16270	PER40	Endodermis	Wendrich et al., Science, 2020
AT5G46600	ALMT13	Endodermis	Wendrich et al., Science, 2020
AT5G57620	MYB36	Endodermis	Kamiya et al., PNAS, 2015
AT5G14750	WER	LRC + Atrichoblast	Birnbaum et al., Science, 2003
AT5G19530	ACL5	Metaxylem	Wendrich et al., Science, 2020
AT2G31310	LBD14	Pericycle Initials	Wendrich et al., Science, 2020
AT1G79430	APL	Phloem	Bonke et al., Nature,2003
AT4G36410	UBC17	Phloem	Wendrich et al., Science, 2020
AT5G04080	AT5G04080	Phloem	Wendrich et al., Science, 2020
AT2G22850	bZIP6	Phloem;Phloem Pole Pericycle	Lee et al., PNAS, 2006; Frank Qasim Machin et al., The Plant Journal, 2019
AT1G04240	SHY2	Procambium + Xylem	Wendrich et al., Science, 2020
AT1G71050	HIPP20	Procambium + Xylem	Wendrich et al., Science, 2020
AT1G71930	VND7	Protoxylem	Wendrich et al., Science, 2020
AT3G25710	TMO5	Protoxylem	Lee et al., PNAS, 2006; Frank Qasim Machin et al., The Plant Journal, 2019
AT4G18780	CESA8	Protoxylem	Wendrich et al., Science, 2020
AT2G04025	RGF3	Proximal Columella	SEMITONES
AT2G18380	GATA20	PSE	Frank Qasim Machin et al., The Plant Journal, 2019
AT5G62940	PEAR1/DOF2.4	PSE	Miyashima et al., Nature, 2019
AT3G20880	AT3G20880	Quiescent Center	Lee et al., PNAS, 2006
AT3G26120	TEL1	Quiescent Center	Denyer et al., Dev Cell, 2019
AT5G60810	RGF1	Quiescent Center	Matsusaki et al., Science, 2010
AT3G55550	LECRKS4	Quiescent Center + Columella	Wendrich et al., Science, 2020
AT3G60650	AT3G60650	Quiescent Center + Columella	Wendrich et al., Science, 2020
AT1G66470	RHD6	Trichoblast	Menand et al., Science, 2007
AT4G13390	EXT12	Trichoblast	Denyer et al., Dev Cell, 2019
AT5G37800	RSL1	Trichoblast	Menand et al., Science, 2007
AT5G49270	COBL9	Trichoblast	Huang et al., Plant Physiol, 2017
AT5G58010	LRL3	Trichoblast	Lee et al., PNAS, 2006
AT2G36120	DOT1	Xylem Pole Pericycle	Wendrich et al., Science, 2020
AT4G30450	XPP	Xylem Pole Pericycle	Wendrich et al., Science, 2020

Locus	Gene	Celltype	Source
<chr>	<chr>	<chr>	<chr>
AT1G79840	GL2	Atrichoblast	Lee et al., PNAS, 2006
AT3G28540	AT3G28540	Columella (1-3th Outer Layer)	Wendrich et al., Science, 2020
AT1G17400	AT1G17400	Columella (1-5th Outer Layer)	Wendrich et al., Science, 2020
AT1G62500	CO2	Cortex	Heidstra et al., GenesDev, 2004
AT2G40260	AT2G40260	Cortex	Wendrich et al., Science, 2020
AT3G61930	AT3G61930	Distal Columella	SEMITONES
AT1G16390	AT1G16390	Endodermis	Wendrich et al., Science, 2020
AT1G30750	AT1G30750	Endodermis	Wendrich et al., Science, 2020
AT3G54220	SCR	Endodermis	Birnbaum et al., Science, 2003
AT4G16270	PER40	Endodermis	Wendrich et al., Science, 2020
AT5G46600	ALMT13	Endodermis	Wendrich et al., Science, 2020
AT5G57620	MYB36	Endodermis	Kamiya et al., PNAS, 2015
AT5G19530	ACL5	Metaxylem	Wendrich et al., Science, 2020
AT2G31310	LBD14	Pericycle Initials	Wendrich et al., Science, 2020
AT1G79430	APL	Phloem	Bonke et al., Nature,2003
AT4G36410	UBC17	Phloem	Wendrich et al., Science, 2020
AT5G04080	AT5G04080	Phloem	Wendrich et al., Science, 2020
AT1G71930	VND7	Protoxylem	Wendrich et al., Science, 2020
AT3G25710	TMO5	Protoxylem	Lee et al., PNAS, 2006; Frank Qasim Machin et al., The Plant Journal, 2019
AT4G18780	CESA8	Protoxylem	Wendrich et al., Science, 2020
AT2G04025	RGF3	Proximal Columella	SEMITONES
AT2G18380	GATA20	PSE	Frank Qasim Machin et al., The Plant Journal, 2019
AT5G62940	PEAR1/DOF2.4	PSE	Miyashima et al., Nature, 2019
AT3G20880	AT3G20880	Quiescent Center	Lee et al., PNAS, 2006
AT3G26120	TEL1	Quiescent Center	Denyer et al., Dev Cell, 2019
AT5G60810	RGF1	Quiescent Center	Matsusaki et al., Science, 2010
AT1G66470	RHD6	Trichoblast	Menand et al., Science, 2007
AT4G13390	EXT12	Trichoblast	Denyer et al., Dev Cell, 2019
AT5G37800	RSL1	Trichoblast	Menand et al., Science, 2007
AT5G49270	COBL9	Trichoblast	Huang et al., Plant Physiol, 2017
AT5G58010	LRL3	Trichoblast	Lee et al., PNAS, 2006
AT2G36120	DOT1	Xylem Pole Pericycle	Wendrich et al., Science, 2020
AT4G30450	XPP	Xylem Pole Pericycle	Wendrich et al., Science, 2020

p_val	avg_logFC	pct.1	pct.2	p_val_adj	cluster	gene	Name
<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<chr>	<chr>	<chr>
0	4.359876	0.976	0.194	0	Transition Domain_Atrichoblast	AT5G01330	PDC3
0	4.304782	0.960	0.078	0	Transition Domain_Atrichoblast	AT1G53130	GRI
0	4.077279	0.981	0.328	0	Transition Domain_Atrichoblast	AT1G41830	SKS6
0	3.882929	0.961	0.175	0	Transition Domain_Atrichoblast	AT5G63800	BGAL6
0	3.805117	0.954	0.229	0	Transition Domain_Atrichoblast	AT3G63470	SCPL40
0	3.644233	0.981	0.125	0	Transition Domain_Atrichoblast	AT1G05660	AT1G05660
0	3.533744	0.787	0.087	0	Transition Domain_Atrichoblast	AT5G51490	PME59
0	3.496127	0.967	0.323	0	Transition Domain_Atrichoblast	AT1G50430	DWF5
0	3.421440	0.963	0.142	0	Transition Domain_Atrichoblast	AT5G44585	AT5G44585
0	3.411451	0.944	0.290	0	Transition Domain_Atrichoblast	AT4G27860	AT4G27860
0	3.385488	0.879	0.191	0	Transition Domain_Atrichoblast	AT1G18193	AT1G18193
0	3.339328	0.970	0.176	0	Transition Domain_Atrichoblast	AT5G02580	AT5G02580
0	3.333372	0.972	0.207	0	Transition Domain_Atrichoblast	AT5G15150	HAT7
0	3.305741	0.982	0.260	0	Transition Domain_Atrichoblast	AT3G08030	AT3G08030
0	3.298523	0.968	0.161	0	Transition Domain_Atrichoblast	AT2G41810	AT2G41810
0	3.281937	0.974	0.181	0	Transition Domain_Atrichoblast	AT1G70560	TAA1
0	3.268023	0.901	0.179	0	Transition Domain_Atrichoblast	AT4G25250	PMEI4
0	3.236872	0.942	0.285	0	Transition Domain_Atrichoblast	AT4G03190	GRH1
0	3.232729	0.960	0.163	0	Transition Domain_Atrichoblast	AT4G15230	ABCG30
0	3.170926	0.976	0.279	0	Transition Domain_Atrichoblast	AT4G22010	sks4
0	3.113909	0.946	0.189	0	Transition Domain_Atrichoblast	AT5G40330	MYB23
0	3.109084	0.925	0.107	0	Transition Domain_Atrichoblast	AT2G37260	WRKY44
0	3.063806	0.809	0.151	0	Transition Domain_Atrichoblast	AT3G62280	AT3G62280
0	3.058033	0.824	0.163	0	Transition Domain_Atrichoblast	AT1G73160	AT1G73160
0	3.049632	0.870	0.147	0	Transition Domain_Atrichoblast	AT5G51500	PME60
0	3.034211	0.828	0.268	0	Transition Domain_Atrichoblast	AT3G52500	AT3G52500
0	3.020852	0.912	0.253	0	Transition Domain_Atrichoblast	AT5G65640	BHLH93
0	3.007434	0.949	0.135	0	Transition Domain_Atrichoblast	AT1G54890	AT1G54890
0	3.006829	0.903	0.145	0	Transition Domain_Atrichoblast	AT2G04090	DTX5
0	3.001145	0.932	0.234	0	Transition Domain_Atrichoblast	AT1G69780	ATHB-13
⋮	⋮	⋮	⋮	⋮	⋮	⋮	⋮
0.005113615	1.3694518	0.147	0.241	1	Transition Domain_Procambium	AT5G17690	TFL2
0.005407906	1.5594735	0.233	0.259	1	Transition Domain_Procambium	AT2G41060	UBA2B
0.005469202	1.4256391	0.221	0.133	1	Transition Domain_Procambium	AT2G17590	AT2G17590
0.005772335	0.7654884	0.319	0.235	1	Transition Domain_Procambium	AT5G56890	AT5G56890
0.005784713	0.8848589	0.442	0.299	1	Transition Domain_Procambium	AT5G54440	TRS130
0.005808582	1.8340622	0.454	0.159	1	Transition Domain_Procambium	AT4G09105	AT4G09105
0.006015583	1.4758978	0.325	0.143	1	Transition Domain_Procambium	AT2G23970	GGP5
0.006147177	0.4576765	0.472	0.223	1	Transition Domain_Procambium	AT4G36530	AT4G36530
0.006345547	1.2288016	0.387	0.175	1	Transition Domain_Procambium	AT4G18375	AT4G18375
0.006457260	0.9352226	0.319	0.218	1	Transition Domain_Procambium	AT1G58150	AT1G58150
0.006540872	1.5822467	0.245	0.232	1	Transition Domain_Procambium	AT4G04190	AT4G04190
0.006547528	0.5522590	0.448	0.272	1	Transition Domain_Procambium	AT2G27210	BSL3
0.006697961	0.7703493	0.399	0.164	1	Transition Domain_Procambium	AT1G63240	AT1G63240
0.007048779	1.1145574	0.135	0.131	1	Transition Domain_Procambium	AT2G22540	SVP
0.007269855	1.5258477	0.387	0.063	1	Transition Domain_Procambium	AT2G25060	ENODL14
0.007315341	0.7692672	0.454	0.147	1	Transition Domain_Procambium	AT2G20850	SRF1
0.007525159	1.4744451	0.258	0.139	1	Transition Domain_Procambium	AT2G09445	AT2G09445
0.007549643	1.5455848	0.270	0.210	1	Transition Domain_Procambium	AT4G09490	AT4G09490
0.007586351	1.2293376	0.331	0.194	1	Transition Domain_Procambium	AT3G23330	PCMP-H32
0.007632690	2.5350602	0.356	0.295	1	Transition Domain_Procambium	AT3G04680	CLPS3
0.007644926	0.9538205	0.282	0.138	1	Transition Domain_Procambium	AT3G16250	PNSB3
0.007939177	1.6851117	0.294	0.239	1	Transition Domain_Procambium	AT3G01600	anac044
0.007994449	1.3394202	0.160	0.256	1	Transition Domain_Procambium	AT3G07740	ADA2A
0.008262217	1.8320488	0.387	0.144	1	Transition Domain_Procambium	AT1G14350	MYB124
0.008604453	0.8478655	0.258	0.237	1	Transition Domain_Procambium	AT5G35100	AT5G35100
0.009338881	0.5846969	0.411	0.221	1	Transition Domain_Procambium	AT3G48120	AT3G48120
0.009371151	1.5723879	0.387	0.273	1	Transition Domain_Procambium	AT1G02750	DI19-2
0.009488593	1.0210781	0.454	0.190	1	Transition Domain_Procambium	AT5G65710	HSL2
0.009539965	0.4416200	0.356	0.115	1	Transition Domain_Procambium	AT4G20940	AT4G20940
0.009594586	0.7898078	0.190	0.236	1	Transition Domain_Procambium	AT2G07776	AT2G07776

p_val	avg_logFC	pct.1	pct.2	p_val_adj	cluster	gene	Name	pct.diff	pct.diff.rank	avg_logFC.rank	combined.rank
<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<chr>	<chr>	<chr>	<dbl>	<dbl>	<dbl>	<dbl>
0.000000e+00	3.5262298	0.675	0.082	0.000000e+00	Elongation_Endodermis	AT3G54220	SCR	0.593	116323.5	123163	239486.5
6.838647e-107	3.8018223	0.838	0.119	1.197652e-102	Transition Domain_Endodermis	AT3G54220	SCR	0.719	122780.5	123801	246581.5
1.170162e-97	0.5555261	0.489	0.110	2.049304e-93	Maturation_Endodermis	AT3G54220	SCR	0.379	91558.0	33211	124769.0
1.348769e-40	2.3336712	0.393	0.118	2.362099e-36	Proliferation Domain_Endodermis	AT3G54220	SCR	0.275	72218.5	114812	187030.5

p_val	avg_logFC	pct.1	pct.2	p_val_adj	cluster	gene	Name	pct.diff	pct.diff.rank	avg_logFC.rank	combined.rank
<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<chr>	<chr>	<chr>	<dbl>	<dbl>	<dbl>	<dbl>
2.457018e-37	1.299689	0.279	0.107	4.302975e-33	Elongation_Endodermis	AT2G36100	CASP1	0.172	50385.0	87181	137566.0
0.000000e+00	4.205272	0.976	0.093	0.000000e+00	Maturation_Endodermis	AT2G36100	CASP1	0.883	124787.5	124388	249175.5

Cell type specific markers¶

Selected Markers for Cell type and developmental stage specific dot plot¶

A tibble: 87 × 12
p_val	avg_logFC	pct.1	pct.2	p_val_adj	cluster	gene	Name	pct.diff	pct.diff.rank	avg_logFC.rank	combined.rank
<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<chr>	<chr>	<chr>	<dbl>	<dbl>	<dbl>	<dbl>
0.000000e+00	2.8800395	0.876	0.121	0.000000e+00	Transition Domain_Atrichoblast	AT1G79840	GL2	0.755	123623.5	120054	243677.5
3.895454e-245	2.0378491	0.587	0.116	6.822109e-241	Elongation_Atrichoblast	AT1G79840	GL2	0.471	104568.0	110077	214645.0
0.000000e+00	4.2214263	0.842	0.107	0.000000e+00	Elongation_Cortex	AT5G64620	C/VIF2	0.735	123209.0	124402	247611.0
0.000000e+00	0.2912310	0.268	0.071	0.000000e+00	Proximal Lateral Root Cap	AT2G04025	RGF3	0.197	55760.5	4826	60586.5
1.511211e-239	0.6067237	0.537	0.140	2.646584e-235	Maturation_Cortex	AT5G64620	C/VIF2	0.397	94449.0	38211	132660.0
0.000000e+00	0.2989555	0.400	0.092	0.000000e+00	Elongation_Pericycle	AT3G25710	BHLH32	0.308	78885.5	5751	84636.5
3.236570e-26	2.6419540	0.372	0.066	5.668206e-22	Elongation_Pericycle	AT2G31310	LBD14	0.306	78378.0	118188	196566.0
0.000000e+00	3.6497667	0.691	0.015	0.000000e+00	Elongation_Xylem	AT4G18780	CESA8	0.676	121223.5	123467	244690.5
0.000000e+00	3.5093015	0.766	0.017	0.000000e+00	Elongation_Xylem	AT1G71930	NAC030	0.749	123507.5	123107	246614.5
0.000000e+00	3.2886888	0.829	0.100	0.000000e+00	Elongation_Xylem	AT3G25710	BHLH32	0.729	123062.0	122300	245362.0
1.023165e-12	1.6169463	0.380	0.114	1.791870e-08	Maturation_Pericycle	AT3G25710	BHLH32	0.266	70486.0	99781	170267.0
0.000000e+00	5.8474096	0.750	0.010	0.000000e+00	Elongation_Endodermis	AT1G16390	OCT3	0.740	123318.5	124975	248293.5
0.000000e+00	5.7307579	0.799	0.022	0.000000e+00	Elongation_Endodermis	AT4G16270	PER40	0.777	123973.5	124969	248942.5
0.000000e+00	4.7560838	0.990	0.044	0.000000e+00	Elongation_Endodermis	AT5G57620	MYB36	0.946	124949.0	124741	249690.0
0.000000e+00	4.5832113	0.728	0.043	0.000000e+00	Elongation_Endodermis	AT5G46600	ALMT13	0.685	121612.0	124655	246267.0
0.000000e+00	3.5262298	0.675	0.082	0.000000e+00	Elongation_Endodermis	AT3G54220	SCR	0.593	116323.5	123163	239486.5
1.722081e-285	0.5823483	0.125	0.088	3.015881e-281	Elongation_Endodermis	AT1G30750	AT1G30750	0.037	23727.5	35894	59621.5
2.457018e-37	1.2996888	0.279	0.107	4.302975e-33	Elongation_Endodermis	AT2G36100	CASP1	0.172	50385.0	87181	137566.0
0.000000e+00	4.3325176	0.893	0.031	0.000000e+00	Elongation_Phloem	AT5G62940	DOF5.6	0.862	124694.5	124487	249181.5
0.000000e+00	4.0380863	0.984	0.032	0.000000e+00	Elongation_Phloem	AT1G79430	APL	0.952	124962.5	124167	249129.5
0.000000e+00	4.0194403	0.997	0.050	0.000000e+00	Elongation_Phloem	AT5G04080	AT5G04080	0.947	124953.5	124147	249100.5
0.000000e+00	3.9999511	0.531	0.014	0.000000e+00	Elongation_Phloem	AT2G18380	GATA20	0.517	109844.0	124121	233965.0
1.034523e-301	4.2939897	0.671	0.034	1.811760e-297	Elongation_Phloem	AT4G36410	UBC17	0.637	119127.0	124458	243585.0
2.081747e-10	0.7236844	0.259	0.121	3.645764e-06	Maturation_Procambium	AT3G25710	BHLH32	0.138	42883.0	48935	91818.0
0.000000e+00	2.6326692	0.879	0.114	0.000000e+00	Proliferation Domain_Atrichoblast	AT1G79840	GL2	0.765	123805.5	118097	241902.5
4.688818e-94	0.4693028	0.172	0.091	8.211527e-90	Proliferation Domain_Atrichoblast	AT2G04025	RGF3	0.081	31408.0	24444	55852.0
0.000000e+00	5.1483876	0.768	0.026	0.000000e+00	Maturation_Trichoblast	AT4G13390	AT4G13390	0.742	123362.5	124879	248241.5
0.000000e+00	4.9697672	0.994	0.063	0.000000e+00	Maturation_Trichoblast	AT5G58010	BHLH82	0.931	124917.0	124818	249735.0
0.000000e+00	3.3588530	0.818	0.093	0.000000e+00	Maturation_Trichoblast	AT1G66470	BHLH83	0.725	122945.5	122583	245528.5
1.783170e-201	2.0249158	0.540	0.069	3.122865e-197	Maturation_Trichoblast	AT5G49270	COBL9	0.471	104622.0	109851	214473.0
⋮	⋮	⋮	⋮	⋮	⋮	⋮	⋮	⋮	⋮	⋮	⋮
1.987023e-25	1.5746564	0.154	0.035	3.479873e-21	Proliferation Domain_Cortex	AT1G17400	AT1G17400	0.119	38962.5	98318	137280.5
2.272772e-259	1.3314433	0.663	0.111	3.980305e-255	Proliferation Domain_Trichoblast	AT1G66470	BHLH83	0.552	113036.0	88698	201734.0
1.633657e-97	2.7366102	0.560	0.080	2.861023e-93	Proliferation Domain_Trichoblast	AT5G37800	BHLH86	0.480	105740.0	118956	224696.0
0.000000e+00	3.5579629	0.979	0.051	0.000000e+00	Maturation_Phloem	AT1G79430	APL	0.928	124906.0	123244	248150.0
0.000000e+00	3.4282083	0.997	0.069	0.000000e+00	Maturation_Phloem	AT5G04080	AT5G04080	0.928	124906.0	122854	247760.0
2.160486e-237	3.4280374	0.815	0.046	3.783659e-233	Maturation_Phloem	AT4G36410	UBC17	0.769	123864.0	122853	246717.0
3.042751e-197	2.7885168	0.588	0.024	5.328771e-193	Maturation_Phloem	AT2G18380	GATA20	0.564	114041.5	119378	233419.5
5.223582e-83	2.6625315	0.513	0.050	9.148059e-79	Maturation_Phloem	AT5G62940	DOF5.6	0.463	103654.5	118384	222038.5

A grouped_df: 37 × 15
p_val	avg_logFC	pct.1	pct.2	p_val_adj	cluster	gene	Name	pct.diff	pct.diff.rank	avg_logFC.rank	combined.rank	source	timezone	celltype
<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<chr>	<chr>	<chr>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<chr>	<chr>
0.000000e+00	2.880039	0.876	0.121	0.000000e+00	Transition Domain_Atrichoblast	AT1G79840	GL2	0.755	123623.5	120054	243677.5	1	Transition Domain	Atrichoblast
0.000000e+00	4.221426	0.842	0.107	0.000000e+00	Elongation_Cortex	AT5G64620	C/VIF2	0.735	123209.0	124402	247611.0	1	Elongation	Cortex
0.000000e+00	4.756084	0.990	0.044	0.000000e+00	Elongation_Endodermis	AT5G57620	MYB36	0.946	124949.0	124741	249690.0	1	Elongation	Endodermis
0.000000e+00	4.332518	0.893	0.031	0.000000e+00	Elongation_Phloem	AT5G62940	DOF5.6	0.862	124694.5	124487	249181.5	1	Elongation	Phloem
0.000000e+00	4.969767	0.994	0.063	0.000000e+00	Maturation_Trichoblast	AT5G58010	BHLH82	0.931	124917.0	124818	249735.0	1	Maturation	Trichoblast
2.947593e-86	2.952604	0.647	0.092	5.162120e-82	Proliferation Domain_Pericycle	AT2G31310	LBD14	0.555	113332.5	120506	233838.5	1	Proliferation Domain	Pericycle
6.838647e-107	3.801822	0.838	0.119	1.197652e-102	Transition Domain_Endodermis	AT3G54220	SCR	0.719	122780.5	123801	246581.5	1	Transition Domain	Endodermis
0.000000e+00	3.994196	0.745	0.065	0.000000e+00	Elongation_Trichoblast	AT5G49270	COBL9	0.680	121400.0	124108	245508.0	1	Elongation	Trichoblast
0.000000e+00	4.157532	0.964	0.079	0.000000e+00	Proximal Columella	AT2G04025	RGF3	0.885	124794.0	124337	249131.0	1	Proximal Columella	Proximal Columella
0.000000e+00	4.351426	0.984	0.031	0.000000e+00	Maturation_Xylem	AT1G71930	NAC030	0.953	124965.5	124507	249472.5	1	Maturation	Xylem
1.633657e-97	2.736610	0.560	0.080	2.861023e-93	Proliferation Domain_Trichoblast	AT5G37800	BHLH86	0.480	105740.0	118956	224696.0	1	Proliferation Domain	Trichoblast
2.160486e-237	3.428037	0.815	0.046	3.783659e-233	Maturation_Phloem	AT4G36410	UBC17	0.769	123864.0	122853	246717.0	1	Maturation	Phloem
0.000000e+00	4.205272	0.976	0.093	0.000000e+00	Maturation_Endodermis	AT2G36100	CASP1	0.883	124787.5	124388	249175.5	1	Maturation	Endodermis
1.317794e-49	5.008885	0.816	0.175	2.307853e-45	Proliferation Domain_Quiescent Center	AT3G26120	TEL1	0.641	119330.0	124834	244164.0	1	Proliferation Domain	Quiescent Center
1.201159e-53	3.742543	0.920	0.122	2.103590e-49	Proliferation Domain_Xylem	AT3G25710	BHLH32	0.798	124225.0	123693	247918.0	1	Proliferation Domain	Xylem
0.000000e+00	4.986413	0.817	0.034	0.000000e+00	Elongation_Atrichoblast	AT3G19320	AT3G19320	0.783	124043.0	124826	248869.0	2	Elongation	Atrichoblast
0.000000e+00	4.448936	0.960	0.084	0.000000e+00	Distal Columella	AT1G05010	ACO4	0.876	124764.5	124589	249353.5	2	Distal Columella	Distal Columella
0.000000e+00	4.449222	0.878	0.075	0.000000e+00	Proximal Lateral Root Cap	AT5G60520	AT5G60520	0.803	124278.5	124590	248868.5	2	Proximal Lateral Root Cap	Proximal Lateral Root Cap
0.000000e+00	4.124382	0.918	0.123	0.000000e+00	Maturation_Cortex	AT4G09760	AT4G09760	0.795	124201.0	124293	248494.0	2	Maturation	Cortex
0.000000e+00	4.145240	0.790	0.072	0.000000e+00	Elongation_Pericycle	AT3G45700	NPF2.4	0.718	122769.0	124316	247085.0	2	Elongation	Pericycle
0.000000e+00	5.872471	0.973	0.016	0.000000e+00	Elongation_Xylem	AT1G79620	AT1G79620	0.957	124974.5	124977	249951.5	2	Elongation	Xylem
0.000000e+00	4.673547	0.957	0.081	0.000000e+00	Maturation_Pericycle	AT5G43180	AT5G43180	0.876	124764.5	124701	249465.5	2	Maturation	Pericycle
0.000000e+00	3.992237	0.915	0.097	0.000000e+00	Maturation_Procambium	AT1G61660	BHLH112	0.818	124424.0	124101	248525.0	2	Maturation	Procambium
0.000000e+00	5.013528	0.962	0.055	0.000000e+00	Elongation_Procambium	AT4G14650	AT4G14650	0.907	124855.0	124836	249691.0	2	Elongation	Procambium
0.000000e+00	4.244605	0.896	0.058	0.000000e+00	Proliferation Domain_Atrichoblast	AT1G27950	LTPG1	0.838	124567.5	124427	248994.5	2	Proliferation Domain	Atrichoblast
0.000000e+00	3.836213	0.955	0.134	0.000000e+00	Maturation_Atrichoblast	AT3G01970	WRKY45	0.821	124448.5	123856	248304.5	2	Maturation	Atrichoblast
0.000000e+00	4.303436	0.883	0.128	0.000000e+00	Distal Lateral Root Cap	AT2G42890	ML2	0.755	123623.5	124462	248085.5	2	Distal Lateral Root Cap	Distal Lateral Root Cap
0.000000e+00	3.424465	0.850	0.110	0.000000e+00	Transition Domain_Trichoblast	AT1G27140	GSTU14	0.740	123318.5	122839	246157.5	2	Transition Domain	Trichoblast
0.000000e+00	3.830770	0.973	0.095	0.000000e+00	Transition Domain_Cortex	AT1G12845	AT1G12845	0.878	124772.5	123849	248621.5	2	Transition Domain	Cortex
0.000000e+00	2.907688	0.855	0.114	0.000000e+00	Transition Domain_Pericycle	AT2G26040	PYL2	0.741	123339.0	120229	243568.0	2	Transition Domain	Pericycle
8.601397e-66	4.336299	0.957	0.065	1.506363e-61	Proliferation Domain_Phloem	AT5G62960	AT5G62960	0.892	124820.0	124493	249313.0	2	Proliferation Domain	Phloem
0.000000e+00	3.372740	0.885	0.119	0.000000e+00	Proliferation Domain_Cortex	AT3G15240	AT3G15240	0.766	123819.0	122643	246462.0	2	Proliferation Domain	Cortex
4.208077e-196	4.268367	0.982	0.074	7.369606e-192	Transition Domain_Phloem	AT2G39830	DAR2	0.908	124861.0	124442	249303.0	2	Transition Domain	Phloem
0.000000e+00	3.494906	0.927	0.213	0.000000e+00	Proliferation Domain_Endodermis	AT3G10610	RPS17C	0.714	122662.5	123065	245727.5	2	Proliferation Domain	Endodermis
6.191777e-70	4.362727	0.919	0.089	1.084366e-65	Transition Domain_Xylem	AT2G34060	PER19	0.830	124523.0	124519	249042.0	2	Transition Domain	Xylem
7.148410e-27	3.877156	0.978	0.174	1.251901e-22	Proliferation Domain_Procambium	AT3G59680	AT3G59680	0.804	124286.5	123915	248201.5	2	Proliferation Domain	Procambium
7.062549e-79	4.503423	0.926	0.055	1.236864e-74	Transition Domain_Procambium	AT4G22900	AT4G22900	0.871	124741.5	124623	249364.5	2	Transition Domain	Procambium